AggV3 allele frequencies¶
Allele Frequencies are available for aggV3 variants on autosomes and chromosome X. The dataset is available in both site-level VCFs and indexed tab-separated files.
Files containing paths to the Allele Frequencies VCF and TSV files are available at s3://512426816668-gel-data-resources/dragen3.7.8/AggV3_resources/manifests/allele_frequencies/2026-08-27/.
Method¶
The bcftools +fill-tags plugin was used to calculate AF, AN, and AC tags from the biallelic aggV3 VCFs. When running bcftools +fill-tags, the --samples-file option was used to enable metric calculations within predefined sample groups. The file supplied to this option contains two columns: the first column specifies the platekey, and the second column contains a comma-separated list of group names to which the sample belongs.
This file is available at:
s3://512426816668-gel-data-resources/dragen3.7.8/AggV3_resources/allele_frequencies_resources/aggv3_consented_samplelist_allele_frequency_groupings_deduplicated_270726.csv
The samples file includes only samples that were consented at the time of processing. Additionally, the remaining 15 duplicate samples were removed using the same deduplication approach as described here.
Sample groups¶
Groups were defined hierarchically, with top-level groupings based on programme source: 100K, NHS-GMS, COVID, and cross-programme. Within each top-level grouping, sub-groups were defined using combinations of the following sample characteristics:
| Characteristic | Description |
|---|---|
| Study source | Rare disease, Cancer, COVID Mild, COVID Severe. |
| Proband status | Whether the sample is the assigned proband in 100K and NHS-GMS rare disease programmes. |
| Inferred genetic ancestry | The sub-population to which a sample has been assigned as described here. Categories include AFR, AMR, EAS, EUR, SAS. |
| Inferred genetic relatedness | Whether the sample was included in the unrelated sub-group, as described here. |
| Sex chromosome karyotype | Sex karyotype ploidy estimates as provided by DRAGEN 3.7.8. Categories include XX, XY. |
For each resulting group, AF, AN, and AC were calculated. The table below summarises the final set of groups, with the group names shown in each cell. These names are used as suffixes for the corresponding AF_*, AN_*, and AC_* INFO fields.
Samples were assigned to every group for which they met the relevant criteria and may therefore contribute to multiple groups. Note that the suffix *_ALL refers to sub-groupings that combine participants from all relevant programmes for a given grouping. For example, UNRELATED_ALL includes all genetically unrelated participants across all 3 programmes (100K, NHS-GMS, and COVID). CANCER_ALL includes all cancer participants across every programme that has a cancer arm which only includes 100K and NHS-GMS.
| Grouping | ALL | 100K | GMS | COVID |
|---|---|---|---|---|
| UNRELATED | UNRELATED_ALL | UNRELATED_100K | UNRELATED_GMS | UNRELATED_COVID |
| UNRELATED_AFR | UNRELATED_AFR_ALL | UNRELATED_AFR_100K | UNRELATED_AFR_GMS | UNRELATED_AFR_COVID |
| UNRELATED_AMR | UNRELATED_AMR_ALL | UNRELATED_AMR_100K | UNRELATED_AMR_GMS | UNRELATED_AMR_COVID |
| UNRELATED_EAS | UNRELATED_EAS_ALL | UNRELATED_EAS_100K | UNRELATED_EAS_GMS | UNRELATED_EAS_COVID |
| UNRELATED_EUR | UNRELATED_EUR_ALL | UNRELATED_EUR_100K | UNRELATED_EUR_GMS | UNRELATED_EUR_COVID |
| UNRELATED_SAS | UNRELATED_SAS_ALL | UNRELATED_SAS_100K | UNRELATED_SAS_GMS | UNRELATED_SAS_COVID |
| AFR | AFR_ALL | AFR_100K | AFR_GMS | AFR_COVID |
| AMR | AMR_ALL | AMR_100K | AMR_GMS | AMR_COVID |
| EAS | EAS_ALL | EAS_100K | EAS_GMS | EAS_COVID |
| EUR | EUR_ALL | EUR_100K | EUR_GMS | EUR_COVID |
| SAS | SAS_ALL | SAS_100K | SAS_GMS | SAS_COVID |
| UNRELATED_CANCER | UNRELATED_CANCER_ALL | UNRELATED_CANCER_100K | UNRELATED_CANCER_GMS | |
| CANCER | CANCER_ALL | CANCER_100K | CANCER_GMS | |
| UNRELATED_RD | UNRELATED_RD_ALL | UNRELATED_RD_100K | UNRELATED_RD_GMS | |
| RD | RD_ALL | RD_100K | RD_GMS | |
| UNRELATED_MILD | UNRELATED_MILD_COVID | |||
| MILD | MILD_COVID | |||
| UNRELATED_SEVERE | UNRELATED_SEVERE_COVID | |||
| SEVERE | SEVERE_COVID | |||
| RD_PROBAND | RD_PROBAND_ALL | RD_PROBAND_100K | RD_PROBAND_GMS | |
| XX | XX_ALL | |||
| XY | XY_ALL |
The table below shows the sample counts for each group based on consent status at the time of the initial release of the allele frequency dataset. These counts represent a snapshot and may fluctuate between releases as consent status changes over time.
| Grouping | ALL | 100K | GMS | COVID |
|---|---|---|---|---|
| Total samples | 134,288 | 86,762 | 26,322 | 21,204 |
| UNRELATED | 99,570 | 60,412 | 18,693 | 20,465 |
| UNRELATED_AFR | 2,813 | 1,689 | 560 | 564 |
| UNRELATED_AMR | 462 | 200 | 109 | 153 |
| UNRELATED_EAS | 1,023 | 451 | 181 | 391 |
| UNRELATED_EUR | 80,841 | 49,603 | 14,394 | 16,844 |
| UNRELATED_SAS | 8,131 | 4,963 | 1,853 | 1,315 |
| AFR | 3,501 | 2,198 | 725 | 578 |
| AMR | 598 | 285 | 160 | 153 |
| EAS | 1,169 | 557 | 218 | 394 |
| EUR | 106,480 | 69,302 | 19,808 | 17,370 |
| SAS | 12,286 | 8,189 | 2,744 | 1,353 |
| UNRELATED_CANCER | 16,336 | 14,685 | 1,651 | |
| CANCER | 16,678 | 14,957 | 1,721 | |
| UNRELATED_RD | 62,769 | 45,727 | 17,042 | |
| RD | 96,406 | 71,805 | 24,601 | |
| UNRELATED_MILD | 13,505 | |||
| MILD | 13,992 | |||
| UNRELATED_SEVERE | 6,960 | |||
| SEVERE | 7,212 | |||
| RD_PROBAND | 46,410 | 33,584 | 12,826 | |
| XX | 68,906 | |||
| XY | 64,827 |